SeqAlto

What is SeqAlto?

SeqAlto is an aligner specifically designed for Illumina reads of length greater
or equal to about 100-bp. It takes advantage of this longer read length to provide
fast alignment rates and accurate placement of polymorphic reads. Paired-end reads
are recommended for even greater accuracy. When aligning 100-bp paired-end reads
SeqAlto is on average about 2-4x faster than BWA while being more sensitive and much
faster for longer reads. Alignment
of Ion Torrent/454 reads is in development.

A commercially-available and fully-supported version of SeqAlto called "Bina Aligner" is available from Bina Technologies and includes additional performance enhancements added by the team at Bina. Please contact Bina Technologies at info@binatechnologies.com for more information on the Bina Aligner. In addition, the Bina team welcomes inquiries for academic collaborations and scientific co-development.

The following is a comparison of the performance when aligning 85 Million 101-bp paired-reads. The benchmark
was run with 8 threads on AWS.